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- Creator:
- Dockham, Andrea Sue
- Description:
- Morphological changes in the Dry Creek (Sonoma County, California) associated with Warm Spring Dam, have reduced habitat availability for rearing fish, and potentially altered the community structure of benthic invertebrates that form the prey-base for juvenile salmonids. I described and compared the structure of benthic invertebrate assemblages and the diets of juvenile steelhead among four stream reaches of Dry Creek downstream of Warm Springs Dam. I hypothesized that if prey availability contributes to factors restricting the success of juvenile salmonids in mainstem Dry Creek, then diet composition should parallel observed differences in reach-specific relative condition and length of juvenile salmonids. Benthic invertebrate assemblages in Dry Creek displayed a longitudinal trend from Warm Springs Dam to the confluence with the Russian River; however, steelhead diet composition did not correspond with reach-specific benthic invertebrate assemblages as expected. Drift-foraging is likely an important feeding strategy for steelhead in mainstem Dry Creek. Steelhead condition and body length corresponded with reach-specific differences in steelhead diet composition. However, reach-specific differences in energetic cost associated with longitudinal differences in water temperature (water temperature was positively correlated with distance from the dam) may be a greater contributor to differences in steelhead size. The relatively high steelhead summer growth rates, in comparison with similar studies, may result from artificially-sustained summer flows in mainstem Dry Creek. Year-round flows in mainstem Dry Creek maintain stream connectivity during a period when non-regulated streams in Mediterranean climates typically become disconnected, therefore increasing food availability and foraging opportunities.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Fisheries
- Creator:
- Brain, Flora H.
- Description:
- Wild Pacific salmon populations are declining throughout California. To strengthen applied salmonid restoration ecology, increased watershed-based understandings of socio-cultural issues thwarting recovery efforts are needed. This study explored perceptions of viabilities of threatened Mattole River salmonids and feelings concerning current human-fish interactions among local residents and fishermen. This qualitative research employed a social constructivist framework and phenomenological orientation. Narrative empirical evidence from lived experience is presented in conjunction with semi-structured interview data from watershed residents, salmon restorationists, poachers, and catch and release fishermen. While many perceive that Mattole coho salmon are facing extinction and consider Chinook salmon’s future nearly as tenuous, a minority of residents believe that Mattole River salmon are abundant. The latter approve and defend salmon poaching, whereas the majority strongly condemns it. Feelings are modulated by perceived threats to the fish runs, and by local identity. Poaching is justified through use of certain neutralization techniques, primarily condemnation of the local nonprofit salmon organization, and claims of local entitlement. The ways people view restoration efforts, poaching, and catch and release fishing in the Mattole River are affected by socio-cultural influences, which constitute barriers to collaborative restoration. Joint fact-finding and listening are among recommendations for trust-building techniques designed to increase recognition of the shared desire for abundant salmon and foster civic response to poaching. The major aim of this research is to inspire improved collaborative and interdisciplinary efforts to address the more significant challenges to salmon recovery, in the Mattole River and beyond.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Environment and Community
- Creator:
- Rizza, Samuel F.
- Description:
- I assessed introgression between sympatric Coastal Cutthroat Trout (Oncorhynchus clarki clarki, CCT) and steelhead (Oncorhynchus mykiss irideus, SH) from 7 sub-basins of the Smith River in northern California. Population, individual and genomic level introgression was determined using a panel of 65 diagnostic single nucleotide polymorphisms, of which 59 are mapped to 26 of 28 known linkage groups. Among hybrids, first-generation (F1) hybrids were rare (2%) and the frequency of backcrosses was asymmetric, with backcrosses to SH infrequent (<1%), and backcrosses to CCT relatively common (17%). Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven by sneak-mating of male CCT with female SH. Genomic clines analysis located nine loci across three known linkage groups that deviated from a neutral model of introgression. Genome-wide differential introgression was documented along with non-random patterns of introgression among linkage groups. These findings suggest genomic blocks are inherited in recent CCT and SH hybrids and subsequently undergo decay as repeated rounds of recombination break up linkage group associations. Chromosome rearrangements known to suppress recombination are suspected in CCT and SH hybrids, and may preserve genomic regions fundamental to isolation. Analysis of geometric morphometrics and phenotypic characteristics revealed distinct CCT and SH morphologies. However, first-generation hybrids and backcrosses expressed non-distinct morphologies that overlapped with parental types, creating challenges in visual field identification.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Fisheries
- Creator:
- Peterson, Matt L.
- Description:
- Steelhead, Oncorhynchus mykiss, exhibit a wide variety of life histories, including a unique “half-pounder” life history, primarily found in Northern California and Southern Oregon. A half-pounder is an immature steelhead that returns to freshwater within about four months of ocean entry. I estimated the frequency of the half-pounder life history among wild and hatchery adult steelhead from the Trinity River using scale analysis. Hatchery smolts currently are released as age-1 smolts from Trinity River Hatchery and are substantially larger than their wild counterparts. Wild smolt ages range from 1 through 3, with most smolts ages 1 or 2. To determine whether age- or size-at-ocean entry affects the tendency for an individual steelhead to exhibit half-pounder life history, I examined over 2,000 scale samples from wild and hatchery adult steelhead collected intermittently over a 27-year period from 1982 through 2009. Age at ocean entry of wild steelhead smolts appeared to be strongly associated with the proportion of adult steelhead returning that have undergone a half-pounder run. Wild smolts entering the ocean as age-1 smolts were more likely to undergo a half-pounder migration than age-2 or age-3 smolts. Based on logistic regression analyses, the size at the end of freshwater zone (prior to estuary or ocean entry) was inversely correlated with half-pounder proportions among returning wild adults. Thus, wild age-2 smolts that were smaller at the end of the freshwater zone were more likely than larger steelhead smolts of the same age to undergo the half-pounder migration. The tendency of hatchery smolts to mature as half-pounders was generally quite low (10-20%), especially in recent years, and appears related to the large size at which steelhead have been released from Trinity River Hatchery since the mid-1990s.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Fisheries
- Creator:
- Naman, Seth
- Description:
- Hatchery fish have been implicated in the decline of stocks of naturally produced anadromous salmonids in the Pacific Northwest. I investigated the extent of predation by hatchery steelhead on naturally produced salmonid fry in the upper-Trinity River, California. During spring of 2007, 315 residualized hatchery steelhead and 1,636 juvenile hatchery steelhead were captured and examined for the presence of salmonid fry in the gut. Residualized steelhead consumed 435 salmonid fry and 2,685 salmonid eggs. Juvenile hatchery steelhead consumed 882 salmonid fry. Predation by juvenile hatchery steelhead was significantly greater near a side channel where a high percentage of adult salmonids were known to spawn. I used mark-recapture techniques to estimate the population of residualized hatchery steelhead and PIT tag recoveries to estimate the population of juvenile hatchery steelhead. Using the population estimates and predation rates, I estimated that 24,194 [95% CI = 21,066-27,323] salmonid fry and 171,018 [95% CI = 155,272-186,764] salmonid eggs were consumed by 2,302 residualized hatchery steelhead in 21 days from 10 February to 2 March 2007. Excluding the results from the side channel, I estimate that 437,697 juvenile hatchery steelhead consumed 61,214 [95% CI = 43,813-78,615] salmonid fry in 30 days from 28 March to 26 April 2007. Assuming a constant population of 1,500 juvenile hatchery steelhead in the side channel during the 30 day period, an additional 49,445 salmonid fry were consumed. Managers should carefully consider all of the risks to naturally produced fish populations from hatchery fish in order to determine if the effects of hatchery releases are consistent with management goals.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Fisheries
- Creator:
- Fuller, Joshua A.
- Description:
- A total of sixty-nine wild juvenile steelhead were surgically implanted with acoustic transmitters and tracked within the estuary and main stem of the Russian River, California, for up to 141 days from mid-July to early December, 2005 and 2006. Each implanted transmitter emitted a unique code that allowed identification of individual steelhead. Estuarine use, movement behavior, and extended estuarine residency were documented using an array of fixed telemetry receiver stations and frequent mobile tracking surveys. Continuous water quality monitoring was conducted throughout the estuary and manual water quality measurements were taken at site specific locations of detected acoustic tagged steelhead during mobile tracking surveys. Manual water quality measurements were used to determine the association of physical parameters (i.e., water quality and depth) with estuarine use. Minimum estuary residence time was derived from the duration of detection and ranged from 4 to 121 days with significant growth occurring with longer residency. Accelerated growth rates in the estuary were observed in scale patterns from untagged and tagged wild steelhead and confirmed by observed growth and scale patterns of three acoustic tagged steelhead that were recaptured after more than 100 days at-large. Estuarine use, movement behavior, extended estuarine residency, and scale patterns of these recaptured steelhead were similar to those of other tagged and untagged steelhead utilizing the same areas of the Russian River estuary. Fall upstream movements of acoustic tagged wild steelhead and captures of untagged estuary steelhead observed aggregating with acoustic tagged steelhead provided evidence that long estuarine residency coupled with accelerated growth resulted in life history traits similar to those of more northern populations in which the half-pounder life history is present. Observed, extended estuarine residency, accelerated growth, and occurrence of half-pounder-like steelhead indicate a very productive rearing environment within the Russian River estuary.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Fisheries
- Creator:
- Ashenfelter, Mark J.
- Description:
- I conducted an experiment to determine if resident rainbow trout (Oncorhynchus mykiss) isolated upstream of a barrier to anadromy in Freshwater Creek, California would exhibit migratory behavior after individuals were relocated to a downstream reach with access to the Pacific Ocean. Between 2005 and 2006 a total sample of 131 age 1+ trout upstream of a 5-m-high waterfall were captured and individually marked with 23-mm passive integrated transponder (PIT) tags. Genetic analysis determined that above-barrier individuals have extensively hybridized with coastal cutthroat trout (Oncorhynchus clarki clarki). At each sampling event, half of the tagged individuals (n=22 and n=43 for trout in 2005 and 2006 respectively) were transplanted approximately 10 km from tidewater. Analysis of otolith microchemistry indicated that above-barrier trout were derived from residential parental lineages. An equal number were released at the point of capture above the barrier. Tagged individuals in above- and below- barrier reaches were subsequently relocated and/or recaptured to track their movement. The majority of transplanted trout displayed little downstream movement from the transplant location. Forty percent of transplanted individuals remained within 500 m of the release location in all sightings. The percentage of transplanted trout that moved into tidally influenced water (6%, or 4 of 65 individuals) did not appear to be different from the percentage of prior downstream resident (4%, or 9 of 210 individuals) that were captured and tagged in the vicinity of the transplant release location and later captured in tidally influenced water. Five, tagged individuals from above the barrier-were detected in below barrier reaches. Four of the transplanted individuals were last detected within the tidally influenced reach of the lower river. Downstream migrant traps captured seven tagged individuals, of which, two were determined to have smolted (one of which was not transplanted below the waterfall) and one was a pre-smolt. The similarity in movements observed in the transplant group and the below-barrier population, the smoltification of transplanted individuals, and the leakage of above-barrier fish downstream suggests the potential for resident trout to exhibit migratory behavior and contribute to breeding populations of steelhead.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Fisheries
- Creator:
- Justice, Casey
- Description:
- Large woody debris is frequently placed into streams of the Pacific Northwest in an effort to improve habitat conditions for rearing juvenile salmonids. Unfortunately, many restoration projects do not incorporate monitoring of biotic response to these activities. This project compared stream reaches and pool habitats with differing quantities of large woody debris to determine the effects of large woody debris restoration structures on biomass, size, growth, and survival of juvenile coho salmon, age-1+ steelhead, and age-0 trout in two coastal streams in Northern California from July 2004 through June 2005. No significant differences in fish response variables were detected between treatment and control reaches. However, some significant relationships between physical habitat features and fish response variables were detected. Biomass and length of age-1+ steelhead were positively related to the proportion of pool habitat, while growth was positively related to mean reach depth. Length of age-0 trout was positively related to large woody debris density during the fall, and growth was positively related to pool depth. Fish responses at the habitat unit scale were more variable, but generally indicated preferences for pools and, in some cases, cover. Overall, the proportion of pool habitat and stream depth appeared to be the most important physical habitat features influencing salmonid productivity in these two coastal streams. Although direct effects of habitat restoration were not detected in this study, these results indicated that stream restoration structures that substantially increase the amount of pool habitat and create deeper pools can positively benefit coho salmon and steelhead populations.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Fisheries
- Creator:
- Clemento, Anthony III
- Description:
- Polymorphic microsatellite markers were employed to explore fine-scale genetic differences between adult summer steelhead trout and juvenile Oncorhynchus mykiss samples collected from the upper Middle Fork Eel River, California. Sampling locations were chosen to capture spatial variation among juveniles within the watershed, and sampling over multiple years allowed estimation of temporal genetic variation for the adult summer steelhead trout group. Tests for Hardy-Weinberg and linkage equilibrium were used to identify significant deviations for each locus and sample population. Kinship and family structure, as estimated by the relatedness coefficient (rxy), effectively explained observed genetic disequilibrium. Analysis revealed minimal genetic variation between the three sample years of adult summer steelhead trout, suggesting that the summer life-history phenotype has a heritable component. Significant genetic differences among juvenile collections from upper Middle Fork Eel tributaries indicated the presence of small, isolated, resident populations. Although closely related to the summer steelhead trout population, these resident groups did not appear to be exchanging migrants with the anadromous form at this time. Within the adult holding habitat, many juveniles assigned to the summer steelhead trout lineage, while others appeared to represent unique groups possibly due to family structure. Comparisons with outgroups from the Eel River, Mendocino Coast and Smith River revealed significant distinctions between groups of O. mykiss sampled at the drainage scale. Overall, sampled populations showed varying degrees of differentiation, indicative of a complex history of gene flow and genetic drift in the Middle Fork Eel.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Fisheries
- Creator:
- DeVault, Brooke
- Description:
- Fish passage improvement is used extensively throughout the Pacific Northwest to expand salmonid habitat to increase threatened salmon stocks. While culvert enhancement projects have been evaluated for physical responses, for example, the ability to withstand 100 year stream flows or support roads, few studies have documented the responses of salmonid populations. This study assessed the effects of two culvert replacements and one culvert enhancement on the abundance and movement of coho salmon (Oncorhynchus kisutch), steelhead (O. mykiss), and cutthroat trout (O. clarkii) within the Freshwater Creek watershed, a small, coastal watershed in northern California. All of the culverts in this study had been previously observed to be impediments to juvenile salmonid movement. Biological data was collected both before and after the culvert replacement on one stream, Graham Gulch. Only post-culvert enhancement data was collected for two other streams, McCready and Cloney Gulches. Biological data collection included out-migrant abundances of juvenile salmonids in the spring, summer juvenile abundances, and juvenile and adult movements. All responses were analyzed using an asymmetrical BACI (Before-After-Control Impact) design. Impact streams were three streams that were treated with culvert enhancement. Control streams were three streams that did not have any culverts present. Few significant differences were found between pre- and post-treatment dataset abundances in Graham Gulch. Spring out-migrant and fish movement data for the pre- and post-treatment dataset indicated that more juvenile trout used the impacted tributary for winter refugia after culvert replacement than before culvert replacement. The number of adult spawners using the tributaries post-culvert replacement did not appear to be increasing. Statistical and graphical analyses of the two-post culvert replacement datasets indicated that juvenile abundances did not differ between the treated tributaries and the control tributaries. Without a pre-culvert enhancement dataset it was difficult to assess the effects of culvert enhancement on salmonid populations.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Fisheries